C. Titus Brown
C. Titus Brown
If you get the following zipfile module `UserWarning`, ``` /home/dl/miniconda3/envs/sourmash/lib/python3.10/zipfile.py:1517: UserWarning: Duplicate name: '.sbt.sourmash_k21.index/internal.0' return self._open_to_write(zinfo, force_zip64=force_zip64) ``` it is most likely caused by the output .zip already existing. You...
from https://github.com/dib-lab/sourmash/issues/1226#issuecomment-748382043, @luizirber says: >The challenge then becomes recalculating the reference sigs with smaller scaled values (100?), and efficiently storing it. JSON + gzip for sigs is at the limit...
motivated by https://github.com/sourmash-bio/sourmash/pull/1891, there's an interesting distinction for Index classes that cannot currently be determined programmatically: does this Index class support **efficient** lazy or on-demand loading of signatures from disk?...
Over in https://github.com/sourmash-bio/sourmash/pull/1837, I'm discovering some fun challenges with manifests 🎉 . first, it turns out that manifests do not contain `seed` or `license` (also see https://github.com/sourmash-bio/sourmash/issues/1846 for motivation and...
not sure it does, currently. ref https://github.com/sourmash-bio/sourmash/issues/1849
from a slack conversation with @luizirber about meaning(s) of `internal_location` - Luiz: >URLs in IPFS are `/ipfs/`, in any case the important thing is the `` >fsspec uses this syntax:...
this came up in conversation with jason stajich over a year ago, and I never stuck it in an issue - it'd be great to have a machine-readable list of...
per https://github.com/sourmash-bio/sourmash/issues/1671#issuecomment-1077585283, we don't have a good way to write signatures to a single file from multiple processes. Such a thing would be nice, but would probably entail some kind...
https://hackmd.io/RScxLBU-SCiEjdNHrJql5w # FracMinHash vs MinHash pseudocode ## FracMinHash Here the `scaled` parameter is tunable, and `H` is the size of the hash space (e.g. 2**64). Note, no hashval >= `H/scaled`...
https://hackmd.io/_h-BqlNWS4uqb9LkiOeALg # Fractional sketches ## or, some details of how sourmash and FracMinHash work! --- Consider overlaps between k-mers extracted from three genomes - two that share sequence, and one...